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Neo4j Graph Data Science :: Algorithms
/*
* Copyright (c) "Neo4j"
* Neo4j Sweden AB [http://neo4j.com]
*
* This file is part of Neo4j.
*
* Neo4j is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see .
*/
package org.neo4j.gds.leiden;
import org.neo4j.gds.api.Graph;
import org.neo4j.gds.collections.haa.HugeAtomicDoubleArray;
import org.neo4j.gds.core.concurrency.Concurrency;
import org.neo4j.gds.core.concurrency.ParallelUtil;
import org.neo4j.gds.core.concurrency.RunWithConcurrency;
import org.neo4j.gds.mem.MemoryEstimation;
import org.neo4j.gds.mem.MemoryEstimations;
import org.neo4j.gds.collections.ha.HugeDoubleArray;
import org.neo4j.gds.collections.ha.HugeLongArray;
import org.neo4j.gds.core.utils.paged.ParallelDoublePageCreator;
import org.neo4j.gds.core.utils.partition.Partition;
import org.neo4j.gds.core.utils.partition.PartitionUtils;
import org.neo4j.gds.core.utils.progress.tasks.ProgressTracker;
import java.util.Optional;
import java.util.concurrent.ExecutorService;
import java.util.stream.LongStream;
public final class ModularityComputer {
static MemoryEstimation estimation() {
return MemoryEstimations.builder(ModularityComputer.class)
.perNode("relationships outside community", HugeAtomicDoubleArray::memoryEstimation)
.perThread("relationship calculator", MemoryEstimations.builder(OutsideRelationshipCalculator.class).build())
.build();
}
private ModularityComputer() {}
static double compute(
Graph workingGraph,
HugeLongArray communities,
HugeDoubleArray communityVolumes,
double gamma,
double coefficient,
Concurrency concurrency,
ExecutorService executorService,
ProgressTracker progressTracker
) {
var relationshipsOutsideCommunity = HugeAtomicDoubleArray.of(workingGraph.nodeCount(), ParallelDoublePageCreator.passThrough(concurrency));
// using degreePartitioning did not show an improvement -- assuming as tasks are too small
var tasks = PartitionUtils.rangePartition(
concurrency,
workingGraph.nodeCount(),
partition -> new OutsideRelationshipCalculator(
partition,
workingGraph,
relationshipsOutsideCommunity,
communities,
progressTracker
), Optional.empty()
);
RunWithConcurrency.builder()
.concurrency(concurrency)
.tasks(tasks)
.executor(executorService)
.run();
double modularity = ParallelUtil.parallelStream(
LongStream.range(0, workingGraph.nodeCount()),
concurrency,
nodeStream ->
nodeStream
.mapToDouble(communityId -> {
double outsideRelationships = relationshipsOutsideCommunity.get(communityId);
double totalRelationships = communityVolumes.get(communityId);
double insideRelationships = totalRelationships - outsideRelationships;
return insideRelationships - totalRelationships * totalRelationships * gamma;
})
.reduce(Double::sum)
.orElseThrow(() -> new RuntimeException("Error while computing modularity"))
);
//we do not have the self-loops from previous merges, so we settle from calculating the outside edges between relationships
//from that and the total sum of weights in communityVolumes we can calculate all inside edges
return modularity * coefficient;
}
static class OutsideRelationshipCalculator implements Runnable {
private final Partition partition;
private final Graph localGraph;
private final HugeAtomicDoubleArray relationshipsOutsideCommunity;
private final HugeLongArray communities;
private final ProgressTracker progressTracker;
OutsideRelationshipCalculator(
Partition partition,
Graph graph,
HugeAtomicDoubleArray relationshipsOutsideCommunity,
HugeLongArray communities,
ProgressTracker progressTracker
) {
this.partition = partition;
this.localGraph = graph.concurrentCopy();
this.relationshipsOutsideCommunity = relationshipsOutsideCommunity;
this.communities = communities;
this.progressTracker = progressTracker;
}
@Override
public void run() {
long startNode = partition.startNode();
long endNode = startNode + partition.nodeCount();
for (long nodeId = startNode; nodeId < endNode; ++nodeId) {
long communityId = communities.get(nodeId);
localGraph.forEachRelationship(nodeId, 1.0, (s, t, w) -> {
long tCommunityId = communities.get(t);
if (tCommunityId != communityId) {
relationshipsOutsideCommunity.getAndAdd(communityId, w);
}
return true;
});
progressTracker.logProgress();
}
}
}
}
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